Responses to injecting drug use have changed focus over the last 20 years. Prevalence and incidence of human immunodeficiency virus (HIV) among people who inject drugs (PWID) in England and Wales were examined in relation to these changes. A voluntary unlinked-anonymous surveillance study obtained a biological sample and questionnaire data from PWID through annual surveys since 1990. Prevalence and incidence trends were estimated via generalised linear models, and compared with a policy time-line. Overall HIV prevalence among 38,539 participations was 1.15%. Prevalence was highest among those who started injecting before 1985; throughout the 1990s, prevalence fell in this group and was stable among those who started injecting later. Prevalence was higher in 2005 than 2000 (odds ratio: 3.56 (95% confidence interval (CI) 1.40–9.03) in London, 3.40 (95% CI 2.31–5.02) elsewhere). Estimated HIV incidence peaked twice, around 1983 and 2005. HIV was an important focus of policy concerning PWID from 1984 until 1998. This focus shifted at a time when drug use and risk were changing. The increased incidence in 2005 cannot be ascribed to the policy changes, but these appeared to be temporally aligned. Policy related to PWID should be continually reviewed to ensure rapid responses to increased risk.